1st EVOLF publication!

1st EVOLF publication by Marieke Westendorp, Jan Stevens et al.

We are excited to share the first EVOLF publication of Bentopy in Protein Science. Bentopy is a workflow for building large-scale models ready for simulation.

Bentopy makes assembling large-scale molecular dynamics models accessible and fast. Building realistic molecular models of cellular environments requires placing proteins, RNA, and metabolites at physiological concentrations within geometrically complex environments.

Bentopy integrates compositional data from proteomics and metabolomics with structural data from cryo-electron tomography and structure prediction to construct simulation-ready molecular models. We demonstrate these capabilities with three systems: a whole bacterial cell, a mitochondrion with compartment-specific compositions, and a SARS-CoV-2 virion in a respiratory aerosol. 

‍Publication: https://onlinelibrary.wiley.com/doi/10.1002/pro.70480

For more information: https://cgmartini.nl/docs/announcements/posts/2026-02-12_bentopy/

Image from an animation of the Syn3A model being filled with RNA, proteins, and metabolites.